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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcactttatactctcgtacttagtgaacataatatgttgaagattttatgaaaagatttcatacagaattacggacatctgtcagcatgaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAAGAAGAACGTGCCTTGTCCAGTGTGCCGGGGGAGGGGTTACATTCTGGAC

Basic information

species Physcomitrella patens
transcript PP1S4_356V6.1
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18351798|gb|BJ183850.1|BJ183850
EST:     TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAG                         GAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGA
genomic: TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAGgtatgtgtcc ... gaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGA
EST: gi|18372258|gb|BJ203860.1|BJ203860
EST:     TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAG                         GAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
genomic: TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAGgtatgtgtcc ... gaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
EST: gi|100450714|gb|CJ974402.1|CJ974402
EST:     TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAG                         GAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTC
genomic: TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAGgtatgtgtcc ... gaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTC
EST: gi|100430651|gb|BY978327.1|BY978327
EST:     TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAG                         GAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
genomic: TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAGgtatgtgtcc ... gaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
EST: gi|100385343|gb|BY950935.1|BY950935
EST:     TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAG                         GAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
genomic: TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAGgtatgtgtcc ... gaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
EST: gi|18359281|gb|BJ191341.1|BJ191341
EST:     TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAG                         GAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
genomic: TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAGgtatgtgtcc ... gaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
EST: gi|100371423|gb|BY967973.1|BY967973
EST:     TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAG                         GAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
genomic: TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAGgtatgtgtcc ... gaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
EST: gi|162168844|gb|FC345042.1|FC345042
EST:     GGCTTAGGCCTCGACATGAAGACAAG                         GAAGCAAGTAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
genomic: GGCTTAGGCCTCGACATGAAGACAAGgtatgtgtcc ... gaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
EST: gi|18364480|gb|BJ196553.1|BJ196553
EST:     TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAG                         GAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA
genomic: TATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAGgtatgtgtcc ... gaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 31 (downstream exon)
Score: 14

GTAGACTATGACCCCTTCGAGGATTTCTTCGGCTTAGGCCTCGACATGAAGACAAGgtatgtgtcc ... gaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAAGAAGAACGTGCCTTGTCCAGTGTGCCGGGGGAGGGGTTACATTCTGGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgaaaagatttcatacagaattacggacatctgtcagcatgaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAAGAAGAACGTGCCTTGTCCAGTGTGCCGGGGGAGGGGTTACATTCTGGAC
                                                ttttc  CT-rich tract
       aaaagattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcactttatactctcgtacttagtgaacataatatgttgaagattttatgaaaagatttcatacagaattacggacatctgtcagcatgaattttcagGAAGCAAGCAGAGAGCATAGATGGCCCTCAGTCTTTCCAGGAGGAATTCAAGAAGAACGTGCCTTGTCCAGTGTGCCGGGGGAGGGGTTACATTCTGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - tgttgaa